If he is otherwise acting normal (eating, pooping, basking, keeping his weight, etc) it could be nightmares. I've had times when I was watching TV with Malygos sleeping on me and he'd go from little dreaming twitches to suddenly waking up, gulping air, puffing his beard, and flopping around. It might be a normal thing he does and you just never noticed before until you were sick and couldn't sleep as well. I know I have a hard time sleeping through the morning cage scrambling if I am sick/get to sleep in. He might also have a hard time sleeping in his salad bowl (not very comfy) or there could be a feeder hiding in his cage. I've had Malygos wake up really late before because a cricket had hidden beneath the tiles and was crawling on him in his sleep. Try giving him a little soft spot to sleep and see if that helps him. Clean, cut-up T-shirts work well or even a little cloth pouch might make him feel safer and sleep better.